Changes between Version 12 and Version 13 of SOPs/variant_calling


Ignore:
Timestamp:
10/15/15 12:45:34 (9 years ago)
Author:
thiruvil
Comment:

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  • SOPs/variant_calling

    v12 v13  
    5757{{{
    5858samtools mpileup -d100000 -Buf /nfs/genomes/sgd_2010/bwa/sacCer3.fa A_reads.bt2.sorted_unique.bam | bcftools call -O b -v -c - >| A_reads.bt2.sorted_unique.raw.bcf
     59#in bcftools call: -m for multi-allelic, -c for bi-alleleic
    5960}}}
    6061Call variants (multiple sample vs. reference) using a set of BAM files